Buildbase BMW pair James Westmoreland and Jon Kirkham were locked in a thrilling duel as they swapped positions in pursuit of fourth place before James Ellison entered the fray on the Milwaukee Yamaha.
Ellison made a stunning recovery after starting from the fifth row of the grid in 17th position to charge through the field.
As the race reached a conclusion, Brookes had moved to the front but the wily Byrne waited until the last corner on the final lap to strike a crucial blow and the 36-year-old held on for the victory.
Brookes was next with Lowes completed the podium positions.
Westmoreland emerged on top of his battle with Kirkham, while Ellison celebrated a well-deserved sixth place finish.
PR Kawasaki's Karl Harris was a solid seventh, with the top ten completed by Bathams Honda rider Michael Rutter, PJ Jacobsen on the Tyco Suzuki and Jakub Smrz on the Padgetts Honda Fireblade.